As a result of the production of a vast amount of genomic sequence from a wide variety of organisms, the next major challenge in genomics is to identify and assemble complete protein sets for each. At the Berkeley Drosophila Genome Project (BDGP) we are actively generating a comprehensive cDNA resource, the Drosophila Gene Collection (DGC) that will contain at least one cDNA for each of the ~13,700 annotated genes. Our cDNA collection has greatly accelerated progress towards a comprehensive transcript map of all Drosophila genes and is being used to determine gene expression patterns in the embryo. Presently, 5,810 cDNA clones comprise the DGC Gold Collection, which is a set of full-length cDNAs that are free of nonsense and missense mutations. We aim to use these cDNA clones to construct two collections of universal donor clones, one with and one without the native stop codon. These collections will be the primary source of high quality open reading frames (ORFs) that will be easy to transfer into a number of different expression vectors. Further, we plan to use the donor clones to make two sets of expression clones, one for use in tissue culture cells and another for use in transgenic flies. Our goals are to obtain a more detailed understanding of the complete set of proteins that are encoded by the Drosophila melanogaster genome and to provide resources for functional genomics and proteomics to the research community. The construction of these clone resources will provide information and tools that will further our understanding of higher eukaryotes and lay the groundwork for more complete analyses of protein function in Drosophila and other eukaryotes, including humans.